If I run 2d class on NS data set with ‘Re-center 2D classes’ = true I get nothing in the end while run the same with this option off getting good classes but not centered.
My guess is something about the re-centering code and the datasign, or the datasign is simply wrong for these particles. You can see a dark spot/negative density is being perfectly centered.
Hello @Elad ,
Thanks for reporting this – could you provide screenshots of the outputs when Re-center 2D classes is set to true? (You can direct message these to me, instead of posting publicly, if you’d prefer).
As well, did you start your processing cryoSPARC with micrographs (through an Import Micrographs or Import Movies job), or with particles (through Import Particle Stack)? Each of these jobs has a build parameter corresponding to whether the data is negatively stained or not, and should be changed in order to correct the data sign for the extracted particles. These parameters are clarified in this negative stain workflow tutorial.
Best regards,
Michael